hrbrmstr
8 years ago
8 changed files with 225 additions and 6 deletions
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#' Compute and display a univariate averaged shifted histogram (polynomial kernel) |
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#' |
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#' See \code{\link[ash]{bin1}} & \code{\link[ash]{ash1}} for more information. |
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#' |
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#' @inheritParams ggplot2::geom_area |
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#' @param geom Use to override the default Geom |
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#' @param ab half-open interval for bins \emph{[a,b)}. If no value is specified, |
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#' the range of x is stretched by \code{5\%} at each end and used the |
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#' interval. |
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#' @param nbin number of bins desired. Default \code{50}. |
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#' @param m integer smoothing parameter; Default \code{5}. |
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#' @param kopt vector of length 2 specifying the kernel, which is proportional |
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#' to \emph{( 1 - abs(i/m)^kopt(1) )i^kopt(2)}; (2,2)=biweight (default); |
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#' (0,0)=uniform; (1,0)=triangle; (2,1)=Epanechnikov; (2,3)=triweight. |
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#' @references David Scott (1992), \emph{"Multivariate Density Estimation,"} |
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#' John Wiley, (chapter 5 in particular).\cr |
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#' \cr |
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#' B. W. Silverman (1986), \emph{"Density Estimation for Statistics |
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#' and Data Analysis,"} Chapman & Hall. |
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#' @section Aesthetics: |
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#' \code{geom_ash} understands the following aesthetics (required aesthetics |
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#' are in bold): |
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#' \itemize{ |
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#' \item \strong{\code{x}} |
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#' \item \code{alpha} |
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#' \item \code{color} |
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#' \item \code{fill} |
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#' \item \code{linetype} |
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#' \item \code{size} |
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#' } |
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#' @section Computed variables: |
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#' \describe{ |
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#' \item{\code{estimate}}{ash estimates} |
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#' } |
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#' @export |
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stat_ash <- function(mapping = NULL, data = NULL, geom = "area", |
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position = "stack", |
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ab = NULL, nbin = 50, m = 5, kopt = c(2, 2), |
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show.legend = NA, inherit.aes = TRUE, ...) { |
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|
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layer( |
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data = data, |
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mapping = mapping, |
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stat = StatAsh, |
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geom = geom, |
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position = position, |
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show.legend = show.legend, |
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inherit.aes = inherit.aes, |
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params = list( |
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ab = ab, |
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nbin = nbin, |
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m = m, |
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kopt = kopt, |
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... |
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) |
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) |
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} |
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|
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#' @export |
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StatAsh <- ggproto("StatAsh", Stat, |
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required_aes = c("x"), |
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default_aes = aes(y = ..estimate.., colour = NA, fill = "gray20", size = 0.5, |
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linetype = 1, alpha = NA), |
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setup_params = function(data, params) { |
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if (!is.null(data$y) || !is.null(params$y)) { |
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stop("stat_ash() must not be used with a y aesthetic.", call. = FALSE) |
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} |
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params |
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}, |
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compute_group = function(data, scales, ab = NULL, |
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nbin = 50, m = 5, kopt = c(2, 2)) { |
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if (is.null(ab)) ab <- nicerange(data$x) |
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bin_res <- ash::bin1(data$x, ab, nbin) |
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ash_msg <- capture.output(ash_res <- ash1(bin_res)) |
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if (ash_res$ier == 1) message("Estimate nonzero outside interval ab.") |
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data.frame(x=ash_res$x, estimate=ash_res$y) |
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} |
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) |
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nicerange <- function (x, beta = 0.1) { |
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ab <- range(x) |
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del <- ((ab[2] - ab[1]) * beta)/2 |
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return(c(ab + c(-del, del))) |
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} |
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After Width: | Height: | Size: 88 KiB |
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% Generated by roxygen2 (4.1.1): do not edit by hand |
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% Please edit documentation in R/geom_ash.r |
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\name{stat_ash} |
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\alias{stat_ash} |
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\title{Compute and display a univariate averaged shifted histogram (polynomial kernel)} |
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\usage{ |
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stat_ash(mapping = NULL, data = NULL, geom = "area", position = "stack", |
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ab = NULL, nbin = 50, m = 5, kopt = c(2, 2), show.legend = NA, |
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inherit.aes = TRUE, ...) |
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} |
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\arguments{ |
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\item{mapping}{Set of aesthetic mappings created by \code{\link{aes}} or |
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\code{\link{aes_}}. If specified and \code{inherit.aes = TRUE} (the |
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default), is combined with the default mapping at the top level of the |
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plot. You only need to supply \code{mapping} if there isn't a mapping |
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defined for the plot.} |
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|
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\item{data}{A data frame. If specified, overrides the default data frame |
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defined at the top level of the plot.} |
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|
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\item{geom}{Use to override the default Geom} |
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|
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\item{position}{Position adjustment, either as a string, or the result of |
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a call to a position adjustment function.} |
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|
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\item{ab}{half-open interval for bins \emph{[a,b)}. If no value is specified, |
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the range of x is stretched by \code{5\%} at each end and used the |
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interval.} |
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|
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\item{nbin}{number of bins desired. Default \code{50}.} |
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|
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\item{m}{integer smoothing parameter; Default \code{5}.} |
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|
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\item{kopt}{vector of length 2 specifying the kernel, which is proportional |
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to \emph{( 1 - abs(i/m)^kopt(1) )i^kopt(2)}; (2,2)=biweight (default); |
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(0,0)=uniform; (1,0)=triangle; (2,1)=Epanechnikov; (2,3)=triweight.} |
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|
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\item{show.legend}{logical. Should this layer be included in the legends? |
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\code{NA}, the default, includes if any aesthetics are mapped. |
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\code{FALSE} never includes, and \code{TRUE} always includes.} |
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|
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\item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, |
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rather than combining with them. This is most useful for helper functions |
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that define both data and aesthetics and shouldn't inherit behaviour from |
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the default plot specification, e.g. \code{\link{borders}}.} |
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|
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\item{...}{other arguments passed on to \code{\link{layer}}. There are |
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three types of arguments you can use here: |
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|
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\itemize{ |
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\item Aesthetics: to set an aesthetic to a fixed value, like |
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\code{color = "red"} or \code{size = 3}. |
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\item Other arguments to the layer, for example you override the |
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default \code{stat} associated with the layer. |
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\item Other arguments passed on to the stat. |
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}} |
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} |
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\description{ |
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See \code{\link[ash]{bin1}} & \code{\link[ash]{ash1}} for more information. |
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} |
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\section{Aesthetics}{ |
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|
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\code{geom_ash} understands the following aesthetics (required aesthetics |
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are in bold): |
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\itemize{ |
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\item \strong{\code{x}} |
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\item \code{alpha} |
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\item \code{color} |
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\item \code{fill} |
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\item \code{linetype} |
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\item \code{size} |
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} |
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} |
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|
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\section{Computed variables}{ |
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|
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\describe{ |
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\item{\code{estimate}}{ash estimates} |
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} |
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} |
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\references{ |
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David Scott (1992), \emph{"Multivariate Density Estimation,"} |
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John Wiley, (chapter 5 in particular).\cr |
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\cr |
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B. W. Silverman (1986), \emph{"Density Estimation for Statistics |
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and Data Analysis,"} Chapman & Hall. |
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} |
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|
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